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FIG. 7 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 7. Aedeagi with aedeagal apodemes, ejaculatory apodemes (B, D, E), lateral views (all to same scale). A. D. macrospina (ex: Magazine Mtn., AR). B. D. macrospina (ex: Rochester, NY). C. D. limpiensis (Limpia Canyon, TX). D. D. trispina. E. D. subfunebris.

FIG. 6 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 6. External details of male terminalia, A–G: Cercal spines, right lateral views; H–K: Surstyli, lateral views. All to same scale. A. D. limpiensis (ex: Limpia Canyon, TX). B. D. limpiensis (ex: Patagonia, Arizona). C. D. macrospina (ex: New Orleans, LA). D. D. macrospina (ex: Piqua, OH), dashed line indicates spine sometimes missing. E. D. subfunebris ex: Pasadena, CA). F. G. D. trispina (ex: Earp, CA), G. showing right cercus with one less spine. H. D. limpiensis (ex: Limpia Canyon, TX). I. D. macrospina (ex: New Orleans, LA). J. D. subfunebris (ex: Pasadena, CA). K. D. trispina (ex: Earp, CA).

FIG. 3 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 3. Drosophila macrospina thorax and abdomen (all ex: Rochester, NY). A. Head and thorax, dorsal. B. Thorax, lateral. C. Abdomen, male. D. Abdomen, female.

FIG. 9 in The Drosophila funebris Species Group in North America (Diptera: Drosophilidae)

FIG. 9. Female terminalia (oviscapts, spermathecal capsules, and minutely scaled oviprovector membrane [internal]) of North American species of the D. funebris group (all to same scale). A. D. funebris (introduced). B. D. limpiensis. C. D. macrospina (spermatheca of limpiensis and macrospina is identical). D. D. subfunebris. E. D. trispina.

Figure 21 in Drosophilidae (Diptera) of the Cook Islands

Figure 21. Distribution map of 12 species of the Drosophila ananassae complex. This map was first published by McEvey & Schiffer (2015) and then updated by them (2018). The discovery of the new species D. rarotongae sp. nov. from the southern group of Cook Islands is indicated on this map. Drosophila ananassae s.str. has pantropical distribution indicated within the pale blue lines, the Ambon type locality is shown. Three or more additional but undescribed species occur in New Guinea (and perhaps also in northern Australia), these are not shown (see McEvey & Schiffer, 2015, for further details).

Figures 22–30 in Drosophilidae (Diptera) of the Cook Islands

Figures 22–30. Hypandria of Drosophila rarotongae sp. nov. and related species: (22) D. atripex, Bali, McE32697; (23) D. monieri, Moorea, AM K.380298; (24) D. ochrogaster, New Caledonia, K.282803; (25) D. schugi, Samoa, K.356978; (26) D. rarotongae, Rarotonga, K.385584; (27) D. phaeopleura, Fiji, K.282923; (28) D. pandora, Lake Placid (near Cairns), ex iso-female strain CAQ425; (29) D. ananassae, Marquesas, K.380299; (30) D. anomalata, Townsville, ex type strain CHC221. Abbreviations, see Figs 13–20 caption.

Figure 2 in Drosophilidae (Diptera) of the Cook Islands

Figure 2. Montane forest terrain of Rarotonga showing the relationship between the three "high elevation" collecting sites in the upper Avatiu valley (circles, details in Table 2), close to the more inaccessible higher mountain peaks which could not be reached during the present survey—Te Manga, Te Atkura, Te Kou, and Maungatea. (Colour photo by Marcus Gleinig, terrain image [Te Kou to Te Manga profile distortion due to steepness of gradient] from Google Earth, June 2019).

Figures 13–20 in Drosophilidae (Diptera) of the Cook Islands

Figures 13–20. Drosophila rarotongae sp. nov. (13) male habitus; (14) arista of AM K.385602; (15) wing of AM K.385592; (16, 17) ventrolateral and dorsal views respectively, of hypandrium of AM K.385594 and K.385584—aed, aedeagus; gon s, gonopodal seta (one of a pair); goncx, gonocoxite; pgt, postgonite; phapod, phallapodeme; pregt, pregonite; pregt proc pregonite process; pregt sens, pregonite sensilla (three sensilla detected on this structure under high power); prens, prensisetae (lower of two series, upper series with two prensisetae); trn bd, transverse band; (18) epandrium of AM K.385594; (19) oviscapt of female AM K.385600; and (20) sex combs on foretarsi of male AM K.385592.

Figures 3–10 in Drosophilidae (Diptera) of the Cook Islands

Figures 3–10. Comparison of Drosophila sp. aff. funebris from Cook Islands (left) and D. funebris (right): (3, 4) lateral views of head; (5, 6) dorsal views of cephalo-chaetotaxy, back of head, and scutum anteriorly; (7, 8) ratio of heavy to light costal setation in third costal section of wing—almost entire in Cook Island specimen, only about 0.4 in D. funebris (see Table 4); and (9–10) costal spine size at subcostal break (second spine of pair broken off in Fig. 9 photo). All specimens in AM: Figs 3, 5, 7, 9—K.471932 (Rarotonga); Figs 4 (K.353509), 6 (K.353514), 8 (K.353510), and 10 (K.353614) (all D. funebris from Johannesburg). Scale is 200 µm.

Figures 34–41 in Drosophilidae (Diptera) of the Cook Islands

Figures 34–41. Scaptodrosophila bryani (Malloch), lateral views of males (34–37, K.393581–82, K.393583) and females (38–40, K.393585–87); anterior, middle, and posterior katepisternal setae (kepst s) indicated (36–37); detail of setae arising from scutellum (ap sctl s, apical scutellar seta, long; b sctl s, basal scutellar seta, short) and posterior part of scutum (41). All with label data: "COOK IS, Mangaia | –21.9531° –157.9148° | 7.ii.2017 ... fruit | Michal Polak" except Figs. 37 and 41: "NT Casuarina urban | 12.3731°S 130.8864°E | fruit compost 28.ix.2009 | S. McEvey & M. Braby". All in AM.

Figures 31–33 in Drosophilidae (Diptera) of the Cook Islands

Figures 31–33. Drosophila bipectinata Duda males, with detail of sex combs of male foreleg. Specimens in AM registered K.385867, K.385864 and K.385869.001 with label data: "COOK IS, Aitutaki | –18.8549° –159.7884° | 10.ii.2017 fruit | Michal Polak".

Supporting Information for: Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

This data repository contains supporting information, data, and code for figures and analysis pipelines the PLOS Biology article: "Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life." <ul> <li>4d_full.treefile: Data underlying Figure 1 (note: tree was plotted as a cladogram and key groups collapsed on iToL; the treefile was not modified) and Figure S1.</li> <li>S2_data.csv: Data underlying Figure 2.</li> <li>S3_data.csv: Data underlying Figure 3.</li> <li>Data underlying Figure 4 is found in Table S4 of supplementary_tables.xlsx in the main manuscript</li> <li>S5_data.csv Data underlying Figure 5</li> <li>S6_data.csv Data underlying Figure S2 </li> <li>illumina_only_assms.tar.gz: Archive of Illumina-only assemblies (FASTA) based on publicy available data that we did not generate. Assemblies generated from our own short-read data have been submitted to NCBI GenBank.</li> <li>illumina_vcfs.tar.gz: Illumina-based variant calls and BED tracks of masked bases.</li> <li>genomes.tar.gz: Genome files, for archival purposes.</li> <li>repeatModeler-lib.tar.gz: RepeatModeler2 libraries.</li> <li>diploid_genomes.tar.gz: diploid genomes and BED tracks of phased regions.</li> <li>trees.tar.gz: phylogenies</li> </ul>

FIG. 15 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 15. Hypandrium, aedeagus and other appendages of representative species of the affinis subgroup (ventral views). A. D. narragansett (ASG 10: paralectotype, Massachusetts); B. D. olmeca (ASG 25: holotype); C. D. tolteca (ASG 23); D. D. narragansett (ASG: Virginia); E. D. olmeca (ASG 25: holotype, detail of B). A–C to same scale; D and E to same scale

FIG. 13 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 13. Epandria and associated structures in representative species of the pseudoobscura subgroup. A. D. cuauhtemoci (ASG 38); B. Detail of A; C. D. persimilis (ASG 36); D. Detail of C; E. D. zapoteca, n. sp. (ASG 20).

FIG. 12 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 12. Epandria and associated structures in representative species of the affinis subgroup. A. D. narragansett (ASG 10); B. Details of A; C. D. olmeca, n. sp. (ASG 25); D. Detail of C; E. D. tolteca (ASG 23).

FIG. 10 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 10. Protarsal male sex combs of species in the D. pseudoobscura subgroup. A. D. cuauhtemoci; B. D. lowei (ASG 40); C. D. maya (ASG 41); D. D. persimilis (ASG 36); E. D. pseudoobscura (ASG 35); F. D. zapoteca (ASG 01). All to the same scale.

FIG. 11 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 11. Epandria (male tergite VIII) and associated structures in representative species of the affinis subgroup. A. D. affinis (ASG 29); B. D. affinis, detail of A; C. D. azteca (ASG 13); D. D. chibcha, n. sp. (ASG 05).

FIG. 9 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 9. Protarsal male sex combs (tarsomeres ta1 and ta2, and ta3 for D. chibcha from Peru) of species in the affinis subgroup. A. D. affinis (ASG 29); B. D. algonquin (ASG 32); C. D. athabasca (ASG 31); D. D. azteca (ASG 13: San Franciso, CA); E. D. azteca (ASG 06: Leticia, Colombia); F. D. chibcha, n. sp. (ASG 04: Zurqui, Costa Rica); G. D. chibcha, n. sp. (ASG 05: Las Alturas, Costa Rica); H. D. chibcha (ASG 07: Rancho Grande, Venezuela); I. D. chibcha (ASG 08: Wayqecha, Peru); J. D. narragansett (ASG 10); K. D. olmeca (ASG 25); L. D. tolteca (ASG 23). All to the same scale.

FIG. 5 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 5. Frontal view of heads of Drosophila narragansett (including seminole, new synonym) and the related species D. olmeca, n. sp. A. D. narragansett, female paralectotype (ASG 11); B. D. narragansett, male paralectotype (ASG 10); C. D. seminole, male holotype; D. D. olmeca, n. sp., male holotype (ASG 25).

FIG. 8 in The Drosophila (Sophophora) obscura species group in the Americas (Diptera: Drosophilidae): review, revisions, and three new species

FIG. 8. Oviscapts and spermathecae (lateral views) of species in the pseudoobscura subgroup, with a detail for D. persimilis. A. D. cuauhtemoci (ASG 39); B. D. lowei (ASG 26); C. D. maya (ASG 19); D. D. persimilis (ASG 37); E. D. pseudoobscura (ASG 34); F. D. zapoteca (ASG 21).